Contacts of the helix formed by residues 542 - 558 (chain C) in PDB entry 1M7X
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 542 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541C GLY* 1.3 71.8 - - - -
543C ALA* 1.3 61.8 + - + +
544C TRP* 3.6 8.5 + - - +
545C GLN* 2.8 43.8 + - - +
546C LYS* 2.7 36.3 + - - +
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Residues in contact with ALA 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C ASP* 1.3 81.2 - - + +
544C TRP* 1.3 63.2 + - - +
546C LYS* 3.4 7.9 + - - +
547C PHE* 3.2 26.7 - - - -
595C TRP* 3.4 32.3 - - + -
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Residues in contact with TRP 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542C ASP* 3.6 8.3 + - - +
543C ALA* 1.3 78.8 - - - +
545C GLN* 1.3 74.6 + - + +
547C PHE* 3.3 5.8 + - - +
548C ALA* 2.7 54.8 + - + +
551C ARG* 3.8 6.0 + - - +
595C TRP* 4.3 20.3 - + + +
659C PRO* 5.1 4.7 - - + -
682C ASP* 3.5 22.0 - - - -
687C HIS 3.3 26.4 + - - -
688C GLY* 3.7 2.3 - - - -
689C SER* 3.7 18.6 - - - +
717C PRO* 3.6 40.2 - - + -
718C LEU* 4.2 13.2 - - + -
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Residues in contact with GLN 545 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C PRO* 6.2 2.5 - - - +
541C GLY* 2.9 16.4 - - - -
542C ASP* 2.8 41.7 + - - +
544C TRP* 1.3 86.5 - - + +
546C LYS* 1.3 57.8 + - - +
548C ALA* 3.8 8.3 - - - -
549C ASN* 2.5 42.2 + - - +
659C PRO* 4.0 19.5 - - + +
718C LEU* 3.6 21.8 - - + -
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Residues in contact with LYS 546 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LEU* 3.5 25.8 - - + +
537C ASP* 2.9 43.7 + - - +
539C MET* 2.9 40.9 + - - +
540C PRO 3.9 1.7 + - - +
541C GLY 3.7 14.1 - - - +
542C ASP 2.7 32.6 + - - +
543C ALA* 3.6 8.3 - - - +
544C TRP 3.3 0.2 - - - -
545C GLN* 1.3 77.2 - - - +
547C PHE* 1.3 65.8 + - + +
550C LEU 3.2 15.8 + - - -
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Residues in contact with PHE 547 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C LEU* 3.4 35.0 - - + -
543C ALA* 3.2 22.7 - - - -
544C TRP 3.3 5.7 + - - +
546C LYS* 1.3 82.1 - - + +
548C ALA* 1.3 57.1 + - - +
550C LEU* 3.7 3.6 - - + +
551C ARG* 2.7 54.1 + - - +
573C ALA* 3.6 13.0 - - + -
595C TRP* 3.5 55.6 - + + +
596C HIS* 3.7 21.1 - + - -
599C VAL* 3.7 19.8 - - + +
686C TYR 5.8 0.2 - - - +
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Residues in contact with ALA 548 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C TRP* 2.7 57.5 + - + +
545C GLN* 3.6 4.3 - - - +
547C PHE* 1.3 74.7 - - - +
549C ASN* 1.3 55.6 + - - +
551C ARG* 3.5 15.2 - - - +
552C ALA 2.9 18.4 + - - -
718C LEU* 2.6 33.5 - - + +
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Residues in contact with ASN 549 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C MET* 2.9 23.7 - - + +
497C PRO* 5.0 2.0 - - - +
500C ARG* 2.7 29.6 + - - -
539C MET* 3.6 11.2 - - + -
540C PRO* 3.2 26.5 + - - +
545C GLN* 2.5 29.6 + - - +
546C LYS 3.7 1.8 - - - +
548C ALA* 1.3 73.6 - - - +
550C LEU* 1.3 54.1 + - - +
552C ALA* 3.2 3.8 + - - +
553C TYR 2.7 31.4 + - - -
718C LEU* 3.1 32.0 - - - +
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Residues in contact with LEU 550 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535C ILE* 3.4 36.6 - - + +
536C LEU* 3.5 30.5 - - + +
539C MET* 3.9 8.0 - - + -
546C LYS 3.2 14.3 + - - +
547C PHE* 3.8 5.6 - - + +
549C ASN* 1.3 78.3 - - - +
551C ARG* 1.3 61.4 + - - +
553C TYR* 3.4 9.0 - - + +
554C TYR* 3.2 60.8 + - + +
570C ASN 4.7 0.2 - - - +
573C ALA* 4.1 21.3 - - + -
599C VAL* 4.7 6.7 - - + -
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Residues in contact with ARG 551 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544C TRP* 3.8 14.6 + - - +
547C PHE* 2.7 29.8 + - - +
548C ALA* 3.5 32.8 - - - +
550C LEU* 1.3 72.3 - - - +
552C ALA* 1.3 63.6 + - - +
554C TYR* 3.1 7.2 + - - +
555C GLY 3.1 17.2 + - - -
595C TRP* 4.8 2.4 - - - -
599C VAL* 5.0 13.0 - - + +
602C LEU* 3.3 29.5 - - + +
681C THR* 3.0 38.5 + - + +
682C ASP* 4.0 5.3 + - - +
686C TYR* 3.5 26.7 + - + -
687C HIS 3.4 20.3 + - - -
688C GLY* 3.1 27.9 - - - +
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Residues in contact with ALA 552 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493C MET* 5.6 0.9 - - + -
548C ALA 2.9 8.5 + - - +
549C ASN* 3.8 4.0 - - - +
551C ARG* 1.3 76.0 - - - +
553C TYR* 1.3 56.8 + - - +
556C TRP* 3.0 17.2 + - - +
657C PHE* 4.5 16.2 - - + -
681C THR* 3.3 3.0 - - - +
718C LEU* 3.0 28.3 - - + +
719C ALA* 3.4 17.5 - - - -
720C THR* 2.9 29.9 - - + +
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Residues in contact with TYR 553 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C TRP* 3.6 26.0 - + - -
489C THR* 3.4 22.1 + - - -
490C LEU* 2.8 31.3 - - + +
493C MET* 3.4 35.6 - - + +
523C LEU* 3.3 30.1 - - + +
535C ILE* 3.9 13.2 - - + -
539C MET* 4.9 1.6 - - + -
549C ASN 2.7 17.2 + - - +
550C LEU* 3.4 15.0 - - + +
552C ALA* 1.3 76.2 - - - +
554C TYR* 1.3 74.5 + + - +
556C TRP* 3.4 10.0 + + - +
557C MET* 2.9 24.7 + - - +
657C PHE* 5.7 0.7 - - - -
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Residues in contact with TYR 554 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C LEU* 3.7 22.8 - - + +
535C ILE* 4.4 5.4 - - - +
550C LEU* 3.3 40.3 - - + +
551C ARG 3.1 7.9 + - - +
553C TYR* 1.3 82.2 - + - +
555C GLY* 1.3 61.3 + - - +
557C MET* 4.1 1.6 - - - -
558C TRP* 2.8 53.9 + + + +
566C LEU* 4.1 10.4 - - + +
570C ASN* 3.2 40.0 + - - +
599C VAL* 4.0 17.7 - - + -
602C LEU* 4.3 6.1 - - + -
603C VAL* 3.9 22.9 - - + -
606C LEU* 3.6 17.0 - - + -
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Residues in contact with GLY 555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551C ARG 3.1 11.6 + - - -
552C ALA 3.3 0.2 + - - -
553C TYR 3.3 0.2 - - - -
554C TYR* 1.3 77.1 - - - +
556C TRP* 1.3 59.8 + - - +
558C TRP* 4.8 0.4 - - - -
559C ALA* 3.5 12.6 + - - +
606C LEU* 4.2 18.1 - - - +
653C VAL* 4.4 0.2 - - - +
679C LEU* 4.8 0.2 - - - -
681C THR* 4.2 2.7 - - - -
720C THR* 3.3 24.4 + - - -
722C TRP* 3.3 24.2 + - - -
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Residues in contact with TRP 556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C TRP* 4.2 20.9 - + - +
489C THR* 4.8 4.9 - - + +
507C LEU* 3.7 40.3 + - + +
552C ALA 3.0 15.5 + - - +
553C TYR* 3.7 11.4 - + - +
554C TYR 3.1 0.2 - - - -
555C GLY* 1.3 77.5 - - - +
557C MET* 1.3 60.3 + - - +
559C ALA* 3.3 3.5 + - - +
560C PHE* 3.0 54.1 + + - +
628C TRP* 4.0 6.1 - + - -
639C LEU* 3.6 39.3 - - + -
641C PHE* 3.5 32.8 - + - -
653C VAL* 5.1 2.2 - - + -
655C SER* 3.0 35.0 - - - +
657C PHE* 3.7 13.9 - + + -
720C THR* 4.6 0.4 - - - -
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Residues in contact with MET 557 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485C TRP* 3.2 40.4 - - + -
521C LEU* 3.2 41.9 - - + +
523C LEU* 3.5 31.4 - - + -
553C TYR* 2.9 19.7 + - + +
554C TYR* 3.3 5.4 + - - +
556C TRP* 1.3 78.3 - - - +
558C TRP* 1.3 90.7 + - + +
559C ALA 3.4 0.5 + - - -
560C PHE* 3.5 2.5 + - - -
564C LYS* 3.0 30.8 + - + -
565C LEU 4.1 12.6 - - - +
566C LEU* 4.6 0.4 - - + -
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Residues in contact with TRP 558 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C SER* 3.7 11.4 + - - -
281C PHE* 5.0 1.1 - + - -
554C TYR* 2.8 53.2 + + + +
555C GLY 4.7 0.2 - - - -
557C MET* 1.3 114.1 - - + +
559C ALA* 1.3 57.9 + - - +
564C LYS* 3.1 35.3 + - + +
566C LEU* 3.9 29.2 - - + -
603C VAL* 4.4 14.6 - - + -
606C LEU* 3.7 36.0 - - + +
607C ASN* 2.9 27.8 + - - -
610C TYR* 3.7 27.6 - + + -
616C MET* 4.2 2.4 - - - +
722C TRP* 3.9 19.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il